NAME

Bio::Tools::Analysis::Protein::Domcut - a wrapper around Domcut server

SYNOPSIS

  use   Bio::Tools::Analysis::Protein::Domcut;
  #get a  Bio::PrimarySeq
  use Bio::PrimarySeq;
  my $seq = Bio::PrimarySeq->new
     (-seq=>'IKLCVNLAILAKAHLIELALAL',
     -primary_id=>'test'); # a Bio::PrimarySeqI object
  my $domcut = Bio::Tools::Analysis::Protein::Domcut->new (-seq=>$seq);
  $domcut->run;
  print $domcut->result;# #raw text to standard out

DESCRIPTION

A module to remotely retrieve predictions of protein domain boundaries. Each residue in the protein receives a score, those better than the significance threshold and at a local minimum receive a rank - i.e., the best minimum is rank 1, the second best minimum is rank2 etc. These correspond to domain boundaries. e.g.,

  my $analysis_object = Bio::Tools::Analysis::Protein::Domcut->new
     (-seq => $seq);

creates a new object. The sequence supplied must be a Bio::PrimarySeq and not a Bio::Seq object.

  $analysis_object->run;

submits the query to the server and obtains raw text output

Given an amino acid sequence the results can be obtained in 4 formats, determined by the argument to the result method

1.

The raw text of the program output

  my $rawdata = $analysis_object->result;
    

2.

A reference to an array of hashes of scores for each state and the assigned state. Each element in the array is a residue (indexed from 0).

  my $data_ref = $analysis_object->result('parsed');
  print "score for helix at residue 2 is $data_ref->[1]{'helix'}\n";
  print "predicted struc  at residue 2 is $data_ref->[1]{'struc}\n";
    

3.

An array of Bio::SeqFeature::Generic objects where each feature is a predicted unit of secondary structure. Only stretches of helix/sheet predictions for longer than 4 residues are defined as helices. So, in order to add features to an existing Bio::Seq object;

  # get a Bio::Seq object
  my $seqobj;
  my $tool = Bio::Tools::Analysis::Protein::Domcut->new
      ( -seq => $seqobj->primary_seq);
  $tool->run;
  my @fts = $tool->result(Bio::SeqFeatureI);
  $seqobj->add_SeqFeature(@fts);
  # if you want  meta sequences as well :
  my $meta = $tool->result('meta');
  $seqobj->primary_seq($meta);
  # can access meta data in a Bio::Seq object via a 
  # call to primary_seq:
  print $seq4->primary_seq->named_submeta_text('Domcut', 1,2), "\n";
    

4.

A Bio::Seq::Meta::Array implementing sequence.

This is a Bio::Seq object that can also hold data about each residue in the sequence. In this case, the sequence can be associated with a single array of Domcut prediction scores. e.g.,

  my $meta_sequence = $analysis_object->result('meta');
  print "scores from residues 10 -20 are ",
      $meta_sequence->submeta_text(10,20), "\n";
    

Many methods common to all analyses are inherited from Bio::Tools::Analysis::SimpleAnalysisBase.

SEE ALSO

Bio::SimpleAnalysisI, Bio::Tools::Analysis::SimpleAnalysisBase, Bio::Seq::Meta::Array, Bio::WebAgent

FEEDBACK

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

  https://github.com/bioperl/bioperl-live/issues

AUTHORS

Richard Adams, Richard.Adams@ed.ac.uk,

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

 Name    : result
 Purpose : To retrieve results of analysis in one of several formats.
 Usage   : $job->result (...)
 Returns : a result created by running an analysis
 Args    : various - see keysin $RESULT_SPEC.